U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

LOC126860558 MED14-independent group 3 enhancer GRCh37_chr9:3478271-3479470 [ Homo sapiens (human) ]

Gene ID: 126860558, updated on 12-Sep-2024

Summary

Go to the top of the page Help
Gene symbol
LOC126860558
Gene description
MED14-independent group 3 enhancer GRCh37_chr9:3478271-3479470
Gene type
biological region
Feature type(s)
regulatory: enhancer
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Summary
This genomic region was validated as an active enhancer by the STARR-seq (self-transcribing active regulatory region sequencing) massively parallel reporter assay (MPRA) in HCT116 colorectal carcinoma cells, where it was defined as a group 3 enhancer that depends on the BRD2, BRD4, P300/CBP and CDK7 cofactors, but it has limited or no dependence on the MED14 core Mediator complex subunit. This locus also includes an accessible chromatin subregion that was validated as an enhancer based on its ability to activate an origin of replication minimal core promoter by the ATAC-STARR-seq (assay for transposase-accessible chromatin with self-transcribing active regulatory region sequencing) MPRA in GM12878 lymphoblastoid cells. [provided by RefSeq, May 2023]
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

Go to the top of the page Help
See LOC126860558 in Genome Data Viewer
Location:
chromosome: 9
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (3478271..3479470)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (3482094..3483293)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (3478271..3479470)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene coactivator associated arginine methyltransferase 1 pseudogene 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:3181301-3181935 Neighboring gene uncharacterized LOC105375959 Neighboring gene long intergenic non-protein coding RNA 1231 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:3290904-3291705 Neighboring gene regulatory factor X3 Neighboring gene VISTA enhancer hs1350 Neighboring gene Sharpr-MPRA regulatory region 5337 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28139 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:3525142-3525758 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19740 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28141 Neighboring gene uncharacterized LOC124902110 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28142 Neighboring gene ReSE screen-validated silencer GRCh37_chr9:3577789-3577989 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr9:3674142-3675341 Neighboring gene RFX3 divergent transcript

Genomic regions, transcripts, and products

Go to the top of the page Help

Go to nucleotide: Graphics FASTA GenBank

Bibliography

Go to the top of the pageHelp

Related articles in PubMed

  1. Differential cofactor dependencies define distinct types of human enhancers. Neumayr C, et al. Nature, 2022 Jun. PMID 35650434, Free PMC Article
  2. ATAC-STARR-seq reveals transcription factor-bound activators and silencers within chromatin-accessible regions of the human genome. Hansen TJ, et al. Genome Res, 2022 Aug 25. PMID 35858748, Free PMC Article

GeneRIFs: Gene References Into Functions

Phenotypes

Go to the top of the page Help

Review eQTL and phenotype association data in this region using PheGenI

Variation

Go to the top of the page Help

See variants in ClinVar

See Variation Viewer (GRCh37.p13)

General gene information

Go to the top of the page Help

Other Names

  • ATAC-STARR-seq lymphoblastoid active region 28140

NCBI Reference Sequences (RefSeq)

Go to the top of the page Help

NEW Try the new Transcript table

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_085058.1 

    Range
    101..1300
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000009.12 Reference GRCh38.p14 Primary Assembly

    Range
    3478271..3479470
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060933.1 Alternate T2T-CHM13v2.0

    Range
    3482094..3483293
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

Molecular Biology Databases